Im not much of a speculator, but i had pondered the same type of questions before. My theory is that the so-called "hitchhiker" may be the flood themselves.Think about it!!In the end cinematic, the longsword fighter is sitting perfectly open.surely if the flood are as intelligant as they are made out to be, then they would have been at least inspecting the vehicle, possibly even planning to use it for some sort of travel. after all, they were planning on using the PoA for space travel. MC kinda rushes in to the longsword without taking much time to look around(didnt have any).Just an idea. who knows for sure(besides the storywriters of course).Several flood could have easily been on board when the longsword took off, acting as stowaways,waiting for the perfect time to come out of hiding and infest the human home world completely.The "convict" part of this theory is explained in that the flood were responsible in a large way for the destruction of Halo and many inhabitants on it. They would then need some way to expand thir population and grow. Halo can only support so many lifeforms before it becomes overcrowded. After all, the flood are supposedly a very intelligent race.the longsword would have been a very quick and stealthy way to infiltrate a human or covenant homeworld. This is all just very simple and hypothetical (yet very possible and reasonable) speculation.
Just thoughts.